QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea
To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross co...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164125 |
| _version_ | 1855520523144921088 |
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| author | Singh, Vikas Sinha, Pallavi Obala, Jimmy Khan, Aamir W. Chitikineni, Annapurna Saxena, Rachit K. Varshney, Rajeev K. |
| author_browse | Chitikineni, Annapurna Khan, Aamir W. Obala, Jimmy Saxena, Rachit K. Singh, Vikas Sinha, Pallavi Varshney, Rajeev K. |
| author_facet | Singh, Vikas Sinha, Pallavi Obala, Jimmy Khan, Aamir W. Chitikineni, Annapurna Saxena, Rachit K. Varshney, Rajeev K. |
| author_sort | Singh, Vikas |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement. |
| format | Journal Article |
| id | CGSpace164125 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1641252024-12-20T06:19:39Z QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea Singh, Vikas Sinha, Pallavi Obala, Jimmy Khan, Aamir W. Chitikineni, Annapurna Saxena, Rachit K. Varshney, Rajeev K. genetics (clinical) genetics To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement. 2022-06 2024-12-19T12:53:29Z 2024-12-19T12:53:29Z Journal Article https://hdl.handle.net/10568/164125 en Open Access Springer Singh, Vikas; Sinha, Pallavi; Obala, Jimmy; Khan, Aamir W.; Chitikineni, Annapurna; Saxena, Rachit K. and Varshney, Rajeev K. 2022. QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea. Heredity, Volume 128 no. 6 p. 411-419 |
| spellingShingle | genetics (clinical) genetics Singh, Vikas Sinha, Pallavi Obala, Jimmy Khan, Aamir W. Chitikineni, Annapurna Saxena, Rachit K. Varshney, Rajeev K. QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea |
| title | QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea |
| title_full | QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea |
| title_fullStr | QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea |
| title_full_unstemmed | QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea |
| title_short | QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea |
| title_sort | qtl seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea |
| topic | genetics (clinical) genetics |
| url | https://hdl.handle.net/10568/164125 |
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